diff options
Diffstat (limited to 'biology/gffread/gffread-0.12.7.log-13-0-amd64')
| -rw-r--r-- | biology/gffread/gffread-0.12.7.log-13-0-amd64 | 264 |
1 files changed, 0 insertions, 264 deletions
diff --git a/biology/gffread/gffread-0.12.7.log-13-0-amd64 b/biology/gffread/gffread-0.12.7.log-13-0-amd64 deleted file mode 100644 index d28b274e37cf..000000000000 --- a/biology/gffread/gffread-0.12.7.log-13-0-amd64 +++ /dev/null @@ -1,264 +0,0 @@ -build started at Wed Nov 10 14:44:25 CST 2021 -port directory: /usr/ports/wip/gffread -package name: gffread-0.12.7 -building for: FreeBSD 13-0-amd64-default 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 amd64 -maintained by: jwb@FreeBSD.org -Makefile ident: -Poudriere version: 3.3.7_1 -Host OSVERSION: 1300139 -Jail OSVERSION: 1300139 -Job Id: - ----Begin Environment--- -SHELL=/bin/csh -OSVERSION=1300139 -UNAME_v=FreeBSD 13.0-RELEASE-p4 -UNAME_r=13.0-RELEASE-p4 -BLOCKSIZE=K -MAIL=/var/mail/root -MM_CHARSET=UTF-8 -LANG=C.UTF-8 -WARNING_WAIT=0 -STATUS=1 -HOME=/root -PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin -LOCALBASE=/usr/local -USER=root -TRYBROKEN=yes -LIBEXECPREFIX=/usr/local/libexec/poudriere -POUDRIERE_VERSION=3.3.7_1 -MASTERMNT=/usr/local/poudriere/data/.m/13-0-amd64-default/ref -DEV_WARNING_WAIT=0 -POUDRIERE_BUILD_TYPE=bulk -PACKAGE_BUILDING=yes -SAVED_TERM=xterm-256color -GID=0 -UID=0 -PWD=/usr/local/poudriere/data/.m/13-0-amd64-default/ref/.p -NO_WARNING_PKG_INSTALL_EOL=yes -P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS -MASTERNAME=13-0-amd64-default -SCRIPTPREFIX=/usr/local/share/poudriere -OLDPWD=/usr/local/poudriere/data/.m/13-0-amd64-default/ref/.p -SCRIPTPATH=/usr/local/share/poudriere/testport.sh -POUDRIEREPATH=/usr/local/bin/poudriere ----End Environment--- - ----Begin Poudriere Port Flags/Env--- -PORT_FLAGS= -PKGENV=PACKAGES=/tmp/pkgs PKGREPOSITORY=/tmp/pkgs PKGLATESTREPOSITORY=/tmp/pkgs/Latest -FLAVOR= -DEPENDS_ARGS= -MAKE_ARGS= ----End Poudriere Port Flags/Env--- - ----Begin OPTIONS List--- ----End OPTIONS List--- - ---MAINTAINER-- -jwb@FreeBSD.org ---End MAINTAINER-- - ---CONFIGURE_ARGS-- - ---End CONFIGURE_ARGS-- - ---CONFIGURE_ENV-- -MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/wip/gffread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/wip/gffread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/wip/gffread/work/.cache HOME=/wrkdirs/usr/ports/wip/gffread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/wip/gffread/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh ---End CONFIGURE_ENV-- - ---MAKE_ENV-- -XDG_DATA_HOME=/wrkdirs/usr/ports/wip/gffread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/wip/gffread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/wip/gffread/work/.cache HOME=/wrkdirs/usr/ports/wip/gffread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/wip/gffread/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" ---End MAKE_ENV-- - ---PLIST_SUB-- -OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gffread" EXAMPLESDIR="share/examples/gffread" DATADIR="share/gffread" WWWDIR="www/gffread" ETCDIR="etc/gffread" ---End PLIST_SUB-- - ---SUB_LIST-- -PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gffread DOCSDIR=/usr/local/share/doc/gffread EXAMPLESDIR=/usr/local/share/examples/gffread WWWDIR=/usr/local/www/gffread ETCDIR=/usr/local/etc/gffread ---End SUB_LIST-- - ----Begin make.conf--- -USE_PACKAGE_DEPENDS=yes -BATCH=yes -WRKDIRPREFIX=/wrkdirs -PORTSDIR=/usr/ports -PACKAGES=/packages -DISTDIR=/distfiles -FORCE_PACKAGE=yes -PACKAGE_BUILDING=yes -PACKAGE_BUILDING_FLAVORS=yes -#### /usr/local/etc/poudriere.d/make.conf #### -# Added by auto-admin from /usr/local/sbin/port-poudriere-setup -USE_LOCAL_MK=yes -# End auto-admin addition -#### Misc Poudriere #### -.include "/etc/make.conf.ports_env" ----End make.conf--- ---Resource limits-- -cpu time (seconds, -t) unlimited -file size (512-blocks, -f) unlimited -data seg size (kbytes, -d) 33554432 -stack size (kbytes, -s) 524288 -core file size (512-blocks, -c) unlimited -max memory size (kbytes, -m) unlimited -locked memory (kbytes, -l) unlimited -max user processes (-u) 12013 -open files (-n) 1024 -virtual mem size (kbytes, -v) unlimited -swap limit (kbytes, -w) unlimited -socket buffer size (bytes, -b) unlimited -pseudo-terminals (-p) unlimited -kqueues (-k) unlimited -umtx shared locks (-o) unlimited ---End resource limits-- -=======================<phase: check-sanity >============================ -===> License MIT accepted by the user -=========================================================================== -=======================<phase: pkg-depends >============================ -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - not found -===> Installing existing package /packages/All/pkg-1.17.3.pkg -[13-0-amd64-default] Installing pkg-1.17.3... -[13-0-amd64-default] Extracting pkg-1.17.3: .......... done -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Returning to build of gffread-0.12.7 -=========================================================================== -=======================<phase: fetch-depends >============================ -=========================================================================== -=======================<phase: fetch >============================ -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -=========================================================================== -=======================<phase: checksum >============================ -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. -=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz. -=========================================================================== -=======================<phase: extract-depends>============================ -=========================================================================== -=======================<phase: extract >============================ -===> License MIT accepted by the user -===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found -===> Fetching all distfiles required by gffread-0.12.7 for building -===> Extracting for gffread-0.12.7 -=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. -=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz. -=========================================================================== -=======================<phase: patch-depends >============================ -=========================================================================== -=======================<phase: patch >============================ -===> Patching for gffread-0.12.7 -===> Applying FreeBSD patches for gffread-0.12.7 from /usr/ports/wip/gffread/files -=========================================================================== -=======================<phase: build-depends >============================ -===> gffread-0.12.7 depends on package: gmake>=4.3 - not found -===> Installing existing package /packages/All/gmake-4.3_2.pkg -[13-0-amd64-default] Installing gmake-4.3_2... -[13-0-amd64-default] `-- Installing gettext-runtime-0.21... -[13-0-amd64-default] | `-- Installing indexinfo-0.3.1... -[13-0-amd64-default] | `-- Extracting indexinfo-0.3.1: .... done -[13-0-amd64-default] `-- Extracting gettext-runtime-0.21: .......... done -[13-0-amd64-default] Extracting gmake-4.3_2: .......... done -===> gffread-0.12.7 depends on package: gmake>=4.3 - found -===> Returning to build of gffread-0.12.7 -=========================================================================== -=======================<phase: lib-depends >============================ -=========================================================================== -=>> Recording filesystem state for prebuild... done -=======================<phase: configure >============================ -===> gffread-0.12.7 depends on package: gmake>=4.3 - found -===> Configuring for gffread-0.12.7 -=========================================================================== -=======================<phase: build >============================ -===> Building for gffread-0.12.7 -gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gff_utils.cpp -o gff_utils.o -gclib/gff.cpp:37:12: warning: unused variable 'CLASSCODE_J_RANK' [-Wunused-const-variable] -const byte CLASSCODE_J_RANK = 6; // all junctional based overlaps - ^ -c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gffread.cpp -o gffread.o -1 warning generated. -c++ -fstack-protector-strong -o gffread gclib/GBase.o gclib/GArgs.o gclib/GFaSeqGet.o gclib/gdna.o gclib/codons.o gclib/gff.o gclib/GStr.o gclib/GFastaIndex.o gff_utils.o gffread.o -gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -=========================================================================== -=>> Checking for filesystem violations... done -=======================<phase: run-depends >============================ -=========================================================================== -=>> Recording filesystem state for prestage... done -=======================<phase: stage >============================ -===> Staging for gffread-0.12.7 -===> Generating temporary packing list -gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -install -c gffread /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin -strip /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin/gffread -gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7' -====> Compressing man pages (compress-man) -=========================================================================== -====> Running Q/A tests (stage-qa) -====> Checking for pkg-plist issues (check-plist) -===> Parsing plist -===> Checking for items in STAGEDIR missing from pkg-plist -===> Checking for items in pkg-plist which are not in STAGEDIR -===> No pkg-plist issues found (check-plist) -=>> Checking for staging violations... done -=======================<phase: package >============================ -===> Building package for gffread-0.12.7 -install -l rs /tmp/pkgs/gffread-0.12.7.pkg /tmp/pkgs/gffread-0.12.7.txz -=========================================================================== -=>> Recording filesystem state for preinst... done -=======================<phase: install >============================ -===> Installing for gffread-0.12.7 -===> Checking if gffread is already installed -===> Registering installation for gffread-0.12.7 -[13-0-amd64-default] Installing gffread-0.12.7... -=========================================================================== -=>> Checking shared library dependencies - 0x0000000000000001 NEEDED Shared library: [libc++.so.1] - 0x0000000000000001 NEEDED Shared library: [libc.so.7] - 0x0000000000000001 NEEDED Shared library: [libcxxrt.so.1] - 0x0000000000000001 NEEDED Shared library: [libm.so.5] -=======================<phase: deinstall >============================ -===> Deinstalling for gffread -===> Deinstalling gffread-0.12.7 -Updating database digests format: ..... done -Checking integrity... done (0 conflicting) -Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): - -Installed packages to be REMOVED: - gffread: 0.12.7 - -Number of packages to be removed: 1 -[13-0-amd64-default] [1/1] Deinstalling gffread-0.12.7... -[13-0-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done -=========================================================================== -=>> Checking for extra files and directories -[00:00:25] Installing from package -[13-0-amd64-default] Installing gffread-0.12.7... -[13-0-amd64-default] Extracting gffread-0.12.7: .... done -[00:00:25] Cleaning up -===> Cleaning for gffread-0.12.7 -[00:00:25] Deinstalling package -Updating database digests format: . done -Checking integrity... done (0 conflicting) -Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): - -Installed packages to be REMOVED: - gffread: 0.12.7 - -Number of packages to be removed: 1 -[13-0-amd64-default] [1/1] Deinstalling gffread-0.12.7... -[13-0-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done -build of wip/gffread | gffread-0.12.7 ended at Wed Nov 10 14:44:34 CST 2021 -build time: 00:00:09 |